Check simulation sim_4.5
Alessio Crippa
12 February, 2019
Dynamic report for checking simulation design (4.5)
True mean Progression Free Time (PFT)
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 7.11 7.11 6.26 7.11 7.11
---+ 7.11 7.11 6.26 7.11 7.11
--+- 7.11 7.11 6.26 7.11 7.11
--++ 7.11 7.11 6.26 7.11 7.11
-+-- 7.11 7.11 17.01 7.11 7.11
-+-+ 7.11 7.11 17.01 7.11 7.11
-++- 7.11 7.11 17.01 7.11 7.11
-+++ 7.11 7.11 17.01 7.11 7.11
+--- 7.11 7.11 6.26 7.11 7.11
+--+ 7.11 7.11 6.26 7.11 7.11
+-+- 7.11 7.11 6.26 7.11 7.11
+-++ 7.11 7.11 6.26 7.11 7.11
++-- 7.11 7.11 17.01 7.11 7.11
++-+ 7.11 7.11 17.01 7.11 7.11
+++- 7.11 7.11 17.01 7.11 7.11Graduation output
$superiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 1 0 0
TEfus+ 0 0 0 0 0
$inferiority
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0 0 0 0 0
TP53- & AR- 0 0 0 0 0
TP53+ 0 0 0 0 0
DRD+ 0 0 0 0 0
TEfus+ 0 0 0 0 0Final probability of superioriry by signatures and biomarkers subtypes
$p_sign
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 0.70 0.64 0.98 0.73 0.61
TP53- & AR- 0.57 0.33 0.62 0.82 0.61
TP53+ 0.78 0.82 0.97 0.74 0.67
DRD+ 0.82 0.52 1.00 0.82 0.72
TEfus+ 0.33 0.61 0.73 0.50 0.44
$p_type
Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 0.77 0.21 0.08 0.80 0.72
---+ 0.21 0.53 0.27 0.39 0.22
--+- 0.52 0.36 0.10 0.39 0.18
--++ 0.37 0.80 0.40 0.29 0.49
-+-- 0.92 0.68 0.82 0.90 0.74
-+-+ 0.36 0.23 0.77 0.66 0.61
-++- 0.72 0.51 0.99 0.71 0.57
-+++ 0.63 0.55 0.66 0.51 0.52
+--- 0.40 0.68 0.70 0.40 0.65
+--+ 0.29 0.35 0.46 0.18 0.15
+-+- 0.70 0.58 0.54 0.64 0.67
+-++ 0.45 0.79 0.73 0.76 0.65
++-- 0.48 0.20 0.76 0.36 0.36
++-+ 0.60 0.59 0.75 0.66 0.65
+++- 0.72 0.75 0.92 0.66 0.70
Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
---- 115 77 23 17 54 72
---+ 17 9 21 5 11 5
--+- 68 46 37 29 15 12
--++ 31 18 24 10 15 18
-+-- 21 16 13 2 11 7
-+-+ 15 5 5 3 7 10
-++- 5 3 3 4 2 0
-+++ 0 2 1 1 1 0
+--- 7 3 11 7 4 10
+--+ 11 7 14 4 5 4
+-+- 2 4 1 1 0 1
+-++ 10 6 8 8 7 4
++-- 12 4 4 5 6 5
++-+ 4 2 1 2 0 0
+++- 3 2 2 3 0 0 Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all 321 204 168 101 138 148
TP53- & AR- 168 107 62 27 83 94
TP53+ 119 81 76 56 40 35
DRD+ 60 34 29 20 27 22
TEfus+ 88 49 74 33 46 41
Number of events, PT, and rate by subtype (over time)
Number of events, PT, and rate by signature (over time)
Analysis of final simulated results
Sample of 10 rows:
id trt trt2 line subtype delta month0 time_m all TP53- & AR- TP53+ DRD+ TEfus+
1052 941 Enzalutamide Enzalutamide 1 ---- 1 31 0.2072555 1 1 0 0 0
292 266 Docetaxel Docetaxel 1 ---- 1 8 11.9994481 1 1 0 0 0
1148 1025 Control Docetaxel 1 --+- 0 34 2.0000000 1 0 1 0 0
180 161 Abiraterone Abiraterone 1 --+- 1 5 18.7972708 1 0 1 0 0
302 276 Control Docetaxel 1 ---- 1 9 1.7135962 1 1 0 0 0
249 226 Abiraterone Abiraterone 1 ---- 1 7 12.2799178 1 1 0 0 0
207 184 Control Docetaxel 1 ---- 1 6 3.1424093 1 1 0 0 0
547 497 Abiraterone Abiraterone 1 ---- 1 16 2.2093076 1 1 0 0 0
674 610 Enzalutamide Enzalutamide 1 ---- 1 20 4.2736411 1 1 0 0 0
1167 1044 Carboplatin Carboplatin 1 +--+ 1 34 0.4249596 1 0 0 0 1Descriptives
Mean number of progressions and follow-up time:
$all
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 306 2183. 0.140
2 Enzalutamide 182 1388. 0.131
3 Abiraterone 156 1127. 0.138
4 Carboplatin 98 822. 0.119
5 Cabazitaxel 109 838. 0.130
6 Docetaxel 134 979. 0.137
$`TP53- & AR-`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 157 1128. 0.139
2 Enzalutamide 91 731. 0.124
3 Abiraterone 66 432. 0.153
4 Carboplatin 30 182. 0.165
5 Cabazitaxel 65 573. 0.113
6 Docetaxel 81 640. 0.127
$`TP53+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 119 811. 0.147
2 Enzalutamide 76 557. 0.136
3 Abiraterone 60 465. 0.129
4 Carboplatin 56 470. 0.119
5 Cabazitaxel 33 213. 0.155
6 Docetaxel 37 225. 0.165
$`DRD+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 61 374. 0.163
2 Enzalutamide 25 220. 0.114
3 Abiraterone 27 136. 0.199
4 Carboplatin 16 332. 0.0481
5 Cabazitaxel 22 205. 0.108
6 Docetaxel 20 155. 0.129
$`TEfus+`
# A tibble: 6 x 4
trt progressions PT rate
<fct> <dbl> <dbl> <dbl>
1 Control 81 583. 0.139
2 Enzalutamide 49 284. 0.173
3 Abiraterone 66 530. 0.125
4 Carboplatin 32 266. 0.120
5 Cabazitaxel 38 252. 0.151
6 Docetaxel 39 249. 0.157
Kaplan-Meier results:
$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 367 306 4.86 4.18 5.68
trt=Enzalutamide 228 182 5.17 4.27 6.48
trt=Abiraterone 193 156 5.28 4.45 6.46
trt=Carboplatin 113 98 5.67 4.17 7.44
trt=Cabazitaxel 150 109 5.10 4.45 6.31
trt=Docetaxel 160 134 5.23 4.12 6.25
$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 191 157 5.18 4.32 6.75
trt=Enzalutamide 119 91 5.50 3.79 8.09
trt=Abiraterone 73 66 5.32 3.61 8.48
trt=Carboplatin 31 30 4.09 1.43 7.49
trt=Cabazitaxel 93 65 5.39 4.69 8.72
trt=Docetaxel 102 81 5.55 4.12 7.50
$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 139 119 4.07 3.71 5.64
trt=Enzalutamide 91 76 5.06 3.49 6.60
trt=Abiraterone 85 60 5.07 4.58 6.68
trt=Carboplatin 62 56 5.67 4.12 8.12
trt=Cabazitaxel 42 33 5.24 3.08 6.78
trt=Docetaxel 39 37 5.23 3.74 7.21
$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 71 61 4.14 2.99 6.09
trt=Enzalutamide 36 25 5.50 3.10 9.26
trt=Abiraterone 32 27 3.50 2.47 6.67
trt=Carboplatin 20 16 18.40 8.83 NA
trt=Cabazitaxel 32 22 5.10 3.19 17.58
trt=Docetaxel 26 20 4.15 2.74 10.03
$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)
n events median 0.95LCL 0.95UCL
trt=Control 99 81 4.94 3.90 6.77
trt=Enzalutamide 56 49 3.86 2.62 6.48
trt=Abiraterone 87 66 6.44 5.02 8.73
trt=Carboplatin 39 32 6.55 3.06 10.24
trt=Cabazitaxel 47 38 5.24 2.75 9.81
trt=Docetaxel 43 39 4.56 3.57 6.70
